As for water in the door. Usually there are some drain holes in the bottom. They could be plugged with debris. There also may be a rubber plug down there too. I have drilled new holes in doors to drain out water. The seal the runs along the bottom outer edge of the window is likely leaking and letting the water in.
For the wiring harness. Most likely there is a connector on the inside of the car behind the lower kickpanel. You should be able to disconnect there and then get a junkyard harness and replace after you fix the leak.